Thanks Cooper for saying what you said, because the very first thing I thought after reading his post was "Why in the world did a vet put a beardie that has Yellow Fungus on antibiotics?" That's not only unnecessary (unless he also has a bacterial infection of some kind in addition to the Yellow Fungus), but it's very counterproductive to successfully treating and trying to cure the Yellow Fungus!!!
Yellow Fungus is obviously caused by a fungal infection, it's extremely difficult to successfully treat and completely get rid of because it's a systemic fungal infection, not just an external, topical fungal infection. So that's why experienced reptile vets put beardies who are diagnosed with Yellow Fungus on very strong oral and sometimes injectable antifungal medications in conjunction with topical antifungal scrubs/antiseptics and creams/ointments. However, if your beardie was diagnosed with Yellow Fungus and was put on both oral and topical antifungal medications as well as antibiotics at the same time, the antibiotics are most likely going to completely negate the effectiveness of the antifungal medications she's taking, depending on what antibiotics she's on.
The body of a bearded dragon always has certain strains of bacteria living on their external skin, scales, etc. as well as all along the inside of their gastrointestinal tracts, from their mouths down their throats into their stomachs and so on. This "healthy" or "normal" bacteria is always living on and inside their bodies (whenever a Bearded Dragon is healthy and their body is in stasis) and is not in high enough counts to cause any actual infections or illnesses. One of the main purposes of this "normal" or "healthy" bacteria on and inside a bearded dragon is to keep fungi in check, or to keep fungi from growing into large enough counts to cause localized external fungal infections, localized internal fungal infections, and widespread, systemic fungal infections, like Yellow Fungus does, which is why it's extremely hard to irradicate.
So if your beardie has an active Yellow Fungus infection and is being treated with both oral and topical antifungal meds along with antibiotics (for some reason, I have no idea why), if the antibiotics she's on are effective against the "normal" or "healthy" bacteria that lives on and inside her body and that she needs in order to help keep the Yellow Fungus from spreading, then the antibiotics can actually kill off all of her "healthy" bacteria, allowing the fungal infection to spread out of control. Usually vets prescribe Broad-spectrum antibiotics, meaning they are effective in killing many different types of bacteria, so most likely the antibiotics your beardie is on are actually hurting her and keeping the antifungal medications she's on from being effective.
Sorry I went through all of that, but I wanted you to understand why we are both confused by why a veterinarian would give antibiotics to a bearded dragon diagnosed with Yellow Fungus...Even if your beardie does have some kind of bacterial infection on top of the Yellow Fungus infection, which I doubt because you didn't mention it, there are very specific and special steps that need to be taken in order for the antibiotics to not interfere with treating the Yellow Fungus infection, which is by far the more serious and severe problem. They also wouldn't prescribe a broad-spectrum antibiotic, they would most likely do a culture and sensitivity to diagnose the exact bacterial strain that is causing the bacterial infection, and to determine what specific, narrow-spectrum antibiotic would treat the bacteria.
I doubt your beardie is being treated for a bacterial infection, I have heard of veterinarians (and sadly some human medical doctors) prescribing antibiotics for fungal infections, as well as other really counterproductive treatments, but Yellow Fungus is so aggressive and difficult to successfully treat to begin with that this might be a horrible decision for the vet to have made.
Also, Yellow Fungus is extremely contagious, I'm sure you know this. Cooper already gave you excellent advice as to disinfecting everything inside and out, washing your hands after handling either dragon, and what to use as a disinfectant (F10 is best). You may very well have infected your other dragon if you handled the one that has Yellow Fungus and then handled him without washing your hands with a good disinfecting soap, Yellow Fungus is an extremely nasty disease that spreads like wildfire. Hopefully your healthy dragon did not contract the Yellow Fungus, you did the correct thing by
bathing him, but you need to keep a very close eye on him, you know what the signs and symptoms of Yellow Fungus are, so the minute you see anything on him that looks like it might be Yellow Fungus you need to take him for a skin scraping test. Hopefully you won't have to do this though.
I'm sorry this is happening to you, and I'm sorry you already lost one beardie. Yellow Fungus is such a horrible disease and is just so aggressive, I wish someone would work on developing an effective cure sometime soon...